This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Advances in drug design and high throughput screening technologies have led to the design of a number of therapeutics and diagnostic agents that target various intracellular molecules. However, biodelivery of these drugs and diagnostic agents to their right target remains a significant challenge. Nearly 30% of all early stage lead molecules that have high affinity to the target determined by in-vitro testing do not make it to clinical trails due to their inability to reach their intended targets (Lipinski, 2001). Similarly transporting hydrophilic molecules across the blood brain barrier remains an equally challenging problem. Hence, there is a growing effort to develop novel molecules that can pass through biological membranes and can be used as vehicles for efficient drug delivery (Temsamani et al., 2004). During the past decade, several cell penetrating peptides (CPPs) that enable the intracellular delivery of drugs have been identified. These peptides can be derived from proteins and are called protein transduction domains which are known to efficiently transverse biological membranes. Although the actual mechanism of action is not known, it is widely understood that the process is receptor and transporter independent (Derossi et al., 1996). The translocation is also not endocytosis mediated and may target the lipid bilayer directly (Frankel et al., 1988 and Plank et al., 1998). Thus a direct contact between the translocating peptide and the lipid bilayer needs to be established. Experimental observations have noted that during the peptide translocation process, the peptide induces membrane reorganization due to pore formation, fusion and also temporary destabilizations (Mangoni et al., 1996). The present project will focus on the structural mechanisms involved during the translation of CPPs across various membranes. The proposed study encompassed the following specific aims: a) Identification of antimicrobial peptides that possess cell penetrating properties b) explore relationship between sequence composition and cell penetrating ability c) Role of secondary structure in determining cell penetrating ability d) Effect of membrane composition on cell penetrating ability of peptides. The study will be executed as two projects, project-1 will address specific aims a-c and project-2 will address specific aim-d. This study will lead to the understanding of the structure-activity relationships of CPPs when traversing across lipid bilayers.